Starting phenix.real_space_refine on Fri Mar 15 00:10:29 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ply_13506/03_2024/7ply_13506_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ply_13506/03_2024/7ply_13506.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ply_13506/03_2024/7ply_13506_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ply_13506/03_2024/7ply_13506_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ply_13506/03_2024/7ply_13506_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ply_13506/03_2024/7ply_13506.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ply_13506/03_2024/7ply_13506.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ply_13506/03_2024/7ply_13506_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ply_13506/03_2024/7ply_13506_updated.pdb" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.001 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Br 1 7.06 5 P 3 5.49 5 Mg 1 5.21 5 S 62 5.16 5 C 6471 2.51 5 N 1720 2.21 5 O 1891 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 12": "NH1" <-> "NH2" Residue "A GLU 26": "OE1" <-> "OE2" Residue "A ASP 30": "OD1" <-> "OD2" Residue "A TYR 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 95": "OD1" <-> "OD2" Residue "A TYR 127": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 136": "OD1" <-> "OD2" Residue "A GLU 145": "OE1" <-> "OE2" Residue "A TYR 147": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 213": "NH1" <-> "NH2" Residue "A ARG 219": "NH1" <-> "NH2" Residue "A ARG 231": "NH1" <-> "NH2" Residue "A TYR 242": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 254": "OE1" <-> "OE2" Residue "A GLU 256": "OE1" <-> "OE2" Residue "A ARG 343": "NH1" <-> "NH2" Residue "A ASP 344": "OD1" <-> "OD2" Residue "A PHE 432": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 439": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 441": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 442": "OE1" <-> "OE2" Residue "A GLU 450": "OE1" <-> "OE2" Residue "A PHE 465": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 512": "OE1" <-> "OE2" Residue "A GLU 539": "OE1" <-> "OE2" Residue "A PHE 640": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 658": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 671": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 673": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 674": "OD1" <-> "OD2" Residue "A ARG 712": "NH1" <-> "NH2" Residue "A ASP 723": "OD1" <-> "OD2" Residue "A ARG 724": "NH1" <-> "NH2" Residue "A PHE 751": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 789": "NH1" <-> "NH2" Residue "A ARG 792": "NH1" <-> "NH2" Residue "C PHE 21": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 28": "NH1" <-> "NH2" Residue "C PHE 31": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 69": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 72": "OE1" <-> "OE2" Residue "C TYR 143": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 200": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 206": "NH1" <-> "NH2" Residue "C ARG 254": "NH1" <-> "NH2" Residue "C PHE 262": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 266": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 311": "OD1" <-> "OD2" Residue "C GLU 361": "OE1" <-> "OE2" Residue "B PHE 16": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 123": "OE1" <-> "OE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 10149 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 6110 Number of conformers: 1 Conformer: "" Number of residues, atoms: 748, 6110 Classifications: {'peptide': 748} Link IDs: {'PTRANS': 27, 'TRANS': 720} Chain breaks: 4 Chain: "C" Number of atoms: 2900 Number of conformers: 1 Conformer: "" Number of residues, atoms: 371, 2900 Classifications: {'peptide': 371} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 351} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HIC:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "B" Number of atoms: 1059 Number of conformers: 1 Conformer: "" Number of residues, atoms: 139, 1059 Classifications: {'peptide': 139} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 3, 'TRANS': 135} Chain breaks: 2 Unresolved non-hydrogen bonds: 45 Unresolved non-hydrogen angles: 53 Unresolved non-hydrogen dihedrals: 37 Planarities with less than four sites: {'GLU:plan': 3, 'ARG:plan': 2, 'ASN:plan1': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 31 Chain: "C" Number of atoms: 80 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 80 Unusual residues: {' MG': 1, '9UE': 1, 'ADP': 1, 'PO4': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Time building chain proxies: 5.72, per 1000 atoms: 0.56 Number of scatterers: 10149 At special positions: 0 Unit cell: (106.7, 132, 150.7, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Br 1 34.99 S 62 16.00 P 3 15.00 Mg 1 11.99 O 1891 8.00 N 1720 7.00 C 6471 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 4.04 Conformation dependent library (CDL) restraints added in 1.9 seconds 2474 Ramachandran restraints generated. 1237 Oldfield, 0 Emsley, 1237 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2368 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 60 helices and 12 sheets defined 48.6% alpha, 11.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.21 Creating SS restraints... Processing helix chain 'A' and resid 74 through 76 No H-bonds generated for 'chain 'A' and resid 74 through 76' Processing helix chain 'A' and resid 82 through 95 Processing helix chain 'A' and resid 121 through 127 removed outlier: 3.695A pdb=" N ASN A 125 " --> pdb=" O GLU A 121 " (cutoff:3.500A) Processing helix chain 'A' and resid 139 through 152 Processing helix chain 'A' and resid 165 through 167 No H-bonds generated for 'chain 'A' and resid 165 through 167' Processing helix chain 'A' and resid 169 through 184 Processing helix chain 'A' and resid 193 through 207 Proline residue: A 201 - end of helix Processing helix chain 'A' and resid 247 through 250 No H-bonds generated for 'chain 'A' and resid 247 through 250' Processing helix chain 'A' and resid 260 through 268 removed outlier: 3.567A pdb=" N SER A 268 " --> pdb=" O GLN A 264 " (cutoff:3.500A) Processing helix chain 'A' and resid 275 through 277 No H-bonds generated for 'chain 'A' and resid 275 through 277' Processing helix chain 'A' and resid 286 through 289 No H-bonds generated for 'chain 'A' and resid 286 through 289' Processing helix chain 'A' and resid 301 through 315 Processing helix chain 'A' and resid 319 through 337 removed outlier: 3.741A pdb=" N ASN A 337 " --> pdb=" O LEU A 333 " (cutoff:3.500A) Processing helix chain 'A' and resid 355 through 364 Processing helix chain 'A' and resid 368 through 376 removed outlier: 4.106A pdb=" N CYS A 376 " --> pdb=" O ALA A 372 " (cutoff:3.500A) Processing helix chain 'A' and resid 393 through 423 Processing helix chain 'A' and resid 449 through 479 Processing helix chain 'A' and resid 484 through 486 No H-bonds generated for 'chain 'A' and resid 484 through 486' Processing helix chain 'A' and resid 492 through 500 removed outlier: 3.830A pdb=" N ASN A 497 " --> pdb=" O PRO A 494 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N GLU A 500 " --> pdb=" O ASN A 497 " (cutoff:3.500A) Processing helix chain 'A' and resid 505 through 514 removed outlier: 3.620A pdb=" N LYS A 514 " --> pdb=" O ASP A 510 " (cutoff:3.500A) Processing helix chain 'A' and resid 520 through 531 Processing helix chain 'A' and resid 564 through 568 Processing helix chain 'A' and resid 574 through 581 Processing helix chain 'A' and resid 587 through 592 Processing helix chain 'A' and resid 631 through 633 No H-bonds generated for 'chain 'A' and resid 631 through 633' Processing helix chain 'A' and resid 636 through 652 Processing helix chain 'A' and resid 675 through 684 Processing helix chain 'A' and resid 687 through 695 Processing helix chain 'A' and resid 704 through 713 removed outlier: 4.700A pdb=" N VAL A 713 " --> pdb=" O SER A 709 " (cutoff:3.500A) Processing helix chain 'A' and resid 724 through 735 Processing helix chain 'A' and resid 739 through 741 No H-bonds generated for 'chain 'A' and resid 739 through 741' Processing helix chain 'A' and resid 755 through 791 Processing helix chain 'C' and resid 56 through 60 Processing helix chain 'C' and resid 62 through 64 No H-bonds generated for 'chain 'C' and resid 62 through 64' Processing helix chain 'C' and resid 79 through 91 Processing helix chain 'C' and resid 98 through 100 No H-bonds generated for 'chain 'C' and resid 98 through 100' Processing helix chain 'C' and resid 113 through 125 Processing helix chain 'C' and resid 137 through 145 removed outlier: 3.543A pdb=" N LEU C 142 " --> pdb=" O ALA C 138 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N TYR C 143 " --> pdb=" O VAL C 139 " (cutoff:3.500A) Processing helix chain 'C' and resid 172 through 174 No H-bonds generated for 'chain 'C' and resid 172 through 174' Processing helix chain 'C' and resid 182 through 196 removed outlier: 4.406A pdb=" N GLU C 195 " --> pdb=" O LYS C 191 " (cutoff:3.500A) removed outlier: 4.235A pdb=" N ARG C 196 " --> pdb=" O ILE C 192 " (cutoff:3.500A) Processing helix chain 'C' and resid 203 through 216 removed outlier: 3.745A pdb=" N ILE C 208 " --> pdb=" O ALA C 204 " (cutoff:3.500A) Processing helix chain 'C' and resid 223 through 232 Processing helix chain 'C' and resid 252 through 261 removed outlier: 3.944A pdb=" N CYS C 257 " --> pdb=" O ARG C 254 " (cutoff:3.500A) Proline residue: C 258 - end of helix Processing helix chain 'C' and resid 274 through 284 Processing helix chain 'C' and resid 290 through 295 Processing helix chain 'C' and resid 302 through 304 No H-bonds generated for 'chain 'C' and resid 302 through 304' Processing helix chain 'C' and resid 309 through 320 Processing helix chain 'C' and resid 333 through 348 removed outlier: 4.655A pdb=" N LYS C 336 " --> pdb=" O PRO C 333 " (cutoff:3.500A) removed outlier: 5.145A pdb=" N VAL C 339 " --> pdb=" O LYS C 336 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N GLY C 342 " --> pdb=" O VAL C 339 " (cutoff:3.500A) Processing helix chain 'C' and resid 351 through 354 Processing helix chain 'C' and resid 359 through 365 Processing helix chain 'C' and resid 367 through 373 removed outlier: 3.775A pdb=" N VAL C 370 " --> pdb=" O PRO C 367 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N LYS C 373 " --> pdb=" O VAL C 370 " (cutoff:3.500A) Processing helix chain 'B' and resid 6 through 19 Processing helix chain 'B' and resid 29 through 38 removed outlier: 4.216A pdb=" N GLY B 33 " --> pdb=" O TYR B 29 " (cutoff:3.500A) removed outlier: 4.510A pdb=" N ASP B 34 " --> pdb=" O SER B 30 " (cutoff:3.500A) Processing helix chain 'B' and resid 45 through 52 Processing helix chain 'B' and resid 57 through 62 Processing helix chain 'B' and resid 67 through 78 Proline residue: B 72 - end of helix Processing helix chain 'B' and resid 87 through 96 removed outlier: 4.179A pdb=" N PHE B 96 " --> pdb=" O GLY B 92 " (cutoff:3.500A) Processing helix chain 'B' and resid 106 through 115 Processing helix chain 'B' and resid 122 through 129 Processing helix chain 'B' and resid 141 through 149 Processing sheet with id= A, first strand: chain 'A' and resid 11 through 16 removed outlier: 4.133A pdb=" N ALA A 11 " --> pdb=" O LEU A 27 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N TYR A 50 " --> pdb=" O LEU A 38 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 100 through 103 removed outlier: 3.701A pdb=" N GLY A 236 " --> pdb=" O GLY A 227 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 377 through 382 Processing sheet with id= D, first strand: chain 'A' and resid 547 through 551 Processing sheet with id= E, first strand: chain 'A' and resid 700 through 703 removed outlier: 3.599A pdb=" N SER A 700 " --> pdb=" O PHE A 751 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'A' and resid 340 through 344 removed outlier: 6.901A pdb=" N SER A 347 " --> pdb=" O ARG A 343 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'C' and resid 8 through 11 Processing sheet with id= H, first strand: chain 'C' and resid 35 through 38 Processing sheet with id= I, first strand: chain 'C' and resid 103 through 107 Processing sheet with id= J, first strand: chain 'C' and resid 297 through 300 removed outlier: 6.564A pdb=" N ILE C 151 " --> pdb=" O VAL C 298 " (cutoff:3.500A) removed outlier: 7.978A pdb=" N SER C 300 " --> pdb=" O ILE C 151 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N LEU C 153 " --> pdb=" O SER C 300 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'C' and resid 238 through 241 Processing sheet with id= L, first strand: chain 'B' and resid 26 through 28 452 hydrogen bonds defined for protein. 1260 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.09 Time building geometry restraints manager: 4.39 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 2903 1.33 - 1.46: 2846 1.46 - 1.60: 4514 1.60 - 1.73: 0 1.73 - 1.86: 102 Bond restraints: 10365 Sorted by residual: bond pdb=" C4 9UE C 404 " pdb=" C5 9UE C 404 " ideal model delta sigma weight residual 0.880 1.493 -0.613 2.00e-02 2.50e+03 9.38e+02 bond pdb=" C11 9UE C 404 " pdb=" C12 9UE C 404 " ideal model delta sigma weight residual 2.064 1.523 0.541 2.00e-02 2.50e+03 7.32e+02 bond pdb=" C9 9UE C 404 " pdb=" N1 9UE C 404 " ideal model delta sigma weight residual 1.863 1.361 0.502 2.00e-02 2.50e+03 6.30e+02 bond pdb=" O 9UE C 404 " pdb=" C4 9UE C 404 " ideal model delta sigma weight residual 0.887 1.332 -0.445 2.00e-02 2.50e+03 4.94e+02 bond pdb=" C7 9UE C 404 " pdb=" C8 9UE C 404 " ideal model delta sigma weight residual 1.139 1.518 -0.379 2.00e-02 2.50e+03 3.60e+02 ... (remaining 10360 not shown) Histogram of bond angle deviations from ideal: 97.63 - 105.59: 227 105.59 - 113.55: 5739 113.55 - 121.51: 5876 121.51 - 129.48: 2088 129.48 - 137.44: 68 Bond angle restraints: 13998 Sorted by residual: angle pdb=" C20 9UE C 404 " pdb=" C21 9UE C 404 " pdb=" C28 9UE C 404 " ideal model delta sigma weight residual 73.46 132.01 -58.55 3.00e+00 1.11e-01 3.81e+02 angle pdb=" C20 9UE C 404 " pdb=" C21 9UE C 404 " pdb=" C22 9UE C 404 " ideal model delta sigma weight residual 176.54 122.42 54.12 3.00e+00 1.11e-01 3.25e+02 angle pdb=" C21 9UE C 404 " pdb=" C28 9UE C 404 " pdb="BR 9UE C 404 " ideal model delta sigma weight residual 78.92 131.18 -52.26 3.00e+00 1.11e-01 3.03e+02 angle pdb=" C13 9UE C 404 " pdb=" C14 9UE C 404 " pdb=" C16 9UE C 404 " ideal model delta sigma weight residual 67.70 114.08 -46.38 3.00e+00 1.11e-01 2.39e+02 angle pdb=" N3 9UE C 404 " pdb=" C28 9UE C 404 " pdb="BR 9UE C 404 " ideal model delta sigma weight residual 73.72 117.27 -43.55 3.00e+00 1.11e-01 2.11e+02 ... (remaining 13993 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 32.13: 6076 32.13 - 64.26: 124 64.26 - 96.38: 31 96.38 - 128.51: 6 128.51 - 160.64: 5 Dihedral angle restraints: 6242 sinusoidal: 2568 harmonic: 3674 Sorted by residual: dihedral pdb=" O1B ADP C 401 " pdb=" O3A ADP C 401 " pdb=" PB ADP C 401 " pdb=" PA ADP C 401 " ideal model delta sinusoidal sigma weight residual 300.00 151.78 148.22 1 2.00e+01 2.50e-03 4.44e+01 dihedral pdb=" CA GLY A 563 " pdb=" C GLY A 563 " pdb=" N PHE A 564 " pdb=" CA PHE A 564 " ideal model delta harmonic sigma weight residual 180.00 -150.49 -29.51 0 5.00e+00 4.00e-02 3.48e+01 dihedral pdb=" CA LYS C 61 " pdb=" C LYS C 61 " pdb=" N ARG C 62 " pdb=" CA ARG C 62 " ideal model delta harmonic sigma weight residual -180.00 -150.92 -29.08 0 5.00e+00 4.00e-02 3.38e+01 ... (remaining 6239 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.160: 1505 0.160 - 0.321: 18 0.321 - 0.481: 0 0.481 - 0.641: 1 0.641 - 0.801: 1 Chirality restraints: 1525 Sorted by residual: chirality pdb=" C6 9UE C 404 " pdb=" N 9UE C 404 " pdb=" C29 9UE C 404 " pdb=" C5 9UE C 404 " both_signs ideal model delta sigma weight residual False -2.65 -1.85 -0.80 2.00e-01 2.50e+01 1.60e+01 chirality pdb=" C12 9UE C 404 " pdb=" C11 9UE C 404 " pdb=" C13 9UE C 404 " pdb=" C17 9UE C 404 " both_signs ideal model delta sigma weight residual False 2.99 2.44 0.55 2.00e-01 2.50e+01 7.50e+00 chirality pdb=" C1 9UE C 404 " pdb=" C 9UE C 404 " pdb=" C15 9UE C 404 " pdb=" C2 9UE C 404 " both_signs ideal model delta sigma weight residual False -2.65 -2.40 -0.25 2.00e-01 2.50e+01 1.55e+00 ... (remaining 1522 not shown) Planarity restraints: 1792 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG C 147 " -0.134 9.50e-02 1.11e+02 7.44e-02 2.64e+01 pdb=" NE ARG C 147 " 0.037 2.00e-02 2.50e+03 pdb=" CZ ARG C 147 " -0.084 2.00e-02 2.50e+03 pdb=" NH1 ARG C 147 " 0.030 2.00e-02 2.50e+03 pdb=" NH2 ARG C 147 " 0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 278 " -0.108 9.50e-02 1.11e+02 6.22e-02 2.04e+01 pdb=" NE ARG A 278 " 0.032 2.00e-02 2.50e+03 pdb=" CZ ARG A 278 " -0.074 2.00e-02 2.50e+03 pdb=" NH1 ARG A 278 " 0.026 2.00e-02 2.50e+03 pdb=" NH2 ARG A 278 " 0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA HIS C 88 " -0.019 2.00e-02 2.50e+03 3.71e-02 1.38e+01 pdb=" C HIS C 88 " 0.064 2.00e-02 2.50e+03 pdb=" O HIS C 88 " -0.024 2.00e-02 2.50e+03 pdb=" N THR C 89 " -0.022 2.00e-02 2.50e+03 ... (remaining 1789 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.76: 1758 2.76 - 3.30: 10013 3.30 - 3.83: 16305 3.83 - 4.37: 19307 4.37 - 4.90: 33644 Nonbonded interactions: 81027 Sorted by model distance: nonbonded pdb=" OD2 ASP A 507 " pdb=" OG SER C 350 " model vdw 2.228 2.440 nonbonded pdb=" OH TYR A 456 " pdb=" OE1 GLU A 500 " model vdw 2.246 2.440 nonbonded pdb=" OD1 ASN C 111 " pdb=" NH1 ARG C 177 " model vdw 2.288 2.520 nonbonded pdb=" NZ LYS A 246 " pdb=" OE1 GLN A 639 " model vdw 2.290 2.520 nonbonded pdb=" OE2 GLU A 511 " pdb=" N THR C 351 " model vdw 2.300 2.520 ... (remaining 81022 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.930 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 6.300 Check model and map are aligned: 0.160 Set scattering table: 0.100 Process input model: 31.130 Find NCS groups from input model: 0.270 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.420 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 42.370 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8321 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.016 0.613 10365 Z= 1.078 Angle : 1.492 58.550 13998 Z= 0.680 Chirality : 0.066 0.801 1525 Planarity : 0.008 0.108 1792 Dihedral : 15.961 160.639 3874 Min Nonbonded Distance : 2.228 Molprobity Statistics. All-atom Clashscore : 3.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.16 % Favored : 99.84 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.06 (0.20), residues: 1237 helix: -0.99 (0.17), residues: 605 sheet: -0.26 (0.37), residues: 161 loop : -0.14 (0.26), residues: 471 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.004 TRP C 86 HIS 0.014 0.003 HIS A 260 PHE 0.031 0.003 PHE A 586 TYR 0.036 0.007 TYR A 439 ARG 0.085 0.010 ARG C 147 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2474 Ramachandran restraints generated. 1237 Oldfield, 0 Emsley, 1237 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2474 Ramachandran restraints generated. 1237 Oldfield, 0 Emsley, 1237 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 1093 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 146 time to evaluate : 1.128 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 507 ASP cc_start: 0.7468 (t70) cc_final: 0.6993 (t0) REVERT: C 43 VAL cc_start: 0.9134 (t) cc_final: 0.8692 (p) REVERT: B 32 CYS cc_start: 0.6356 (m) cc_final: 0.5938 (m) outliers start: 0 outliers final: 0 residues processed: 146 average time/residue: 0.2719 time to fit residues: 53.3065 Evaluate side-chains 80 residues out of total 1093 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 80 time to evaluate : 1.182 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 104 optimal weight: 0.6980 chunk 93 optimal weight: 0.8980 chunk 52 optimal weight: 1.9990 chunk 32 optimal weight: 0.6980 chunk 63 optimal weight: 0.5980 chunk 50 optimal weight: 0.7980 chunk 97 optimal weight: 2.9990 chunk 37 optimal weight: 0.0170 chunk 59 optimal weight: 0.7980 chunk 72 optimal weight: 2.9990 chunk 112 optimal weight: 10.0000 overall best weight: 0.5618 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 191 ASN A 264 GLN A 354 HIS A 398 ASN A 406 HIS A 410 ASN A 455 ASN A 497 ASN A 638 HIS A 657 HIS C 137 GLN C 246 GLN B 75 GLN B 147 HIS Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8264 moved from start: 0.2175 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 10365 Z= 0.205 Angle : 0.852 46.924 13998 Z= 0.373 Chirality : 0.043 0.264 1525 Planarity : 0.004 0.054 1792 Dihedral : 12.334 168.900 1396 Min Nonbonded Distance : 2.211 Molprobity Statistics. All-atom Clashscore : 6.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.16 % Favored : 99.84 % Rotamer: Outliers : 1.02 % Allowed : 5.27 % Favored : 93.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.04 (0.23), residues: 1237 helix: 1.05 (0.20), residues: 611 sheet: 0.23 (0.39), residues: 158 loop : 0.62 (0.28), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 79 HIS 0.007 0.001 HIS C 275 PHE 0.019 0.001 PHE C 255 TYR 0.018 0.001 TYR A 758 ARG 0.006 0.001 ARG A 41 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2474 Ramachandran restraints generated. 1237 Oldfield, 0 Emsley, 1237 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2474 Ramachandran restraints generated. 1237 Oldfield, 0 Emsley, 1237 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 1093 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 105 time to evaluate : 1.307 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 10 TYR cc_start: 0.7700 (m-80) cc_final: 0.7497 (m-80) REVERT: A 507 ASP cc_start: 0.7435 (t70) cc_final: 0.6972 (t0) REVERT: A 790 MET cc_start: 0.2418 (tpp) cc_final: 0.1909 (tpt) REVERT: C 123 MET cc_start: 0.7914 (mmm) cc_final: 0.7553 (mmm) REVERT: B 36 MET cc_start: 0.8856 (mtt) cc_final: 0.8520 (mmm) REVERT: B 105 MET cc_start: 0.8370 (OUTLIER) cc_final: 0.7543 (tpp) outliers start: 11 outliers final: 2 residues processed: 109 average time/residue: 0.1730 time to fit residues: 28.8578 Evaluate side-chains 83 residues out of total 1093 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 80 time to evaluate : 1.126 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 159 VAL Chi-restraints excluded: chain C residue 354 GLN Chi-restraints excluded: chain B residue 105 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 62 optimal weight: 2.9990 chunk 34 optimal weight: 0.7980 chunk 93 optimal weight: 2.9990 chunk 76 optimal weight: 0.4980 chunk 31 optimal weight: 1.9990 chunk 112 optimal weight: 0.0980 chunk 121 optimal weight: 10.0000 chunk 100 optimal weight: 0.9980 chunk 111 optimal weight: 7.9990 chunk 38 optimal weight: 1.9990 chunk 90 optimal weight: 1.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 88 ASN C 121 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8301 moved from start: 0.2642 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 10365 Z= 0.254 Angle : 0.806 47.301 13998 Z= 0.347 Chirality : 0.042 0.241 1525 Planarity : 0.004 0.054 1792 Dihedral : 11.718 158.052 1396 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 6.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.73 % Favored : 99.27 % Rotamer: Outliers : 1.20 % Allowed : 7.30 % Favored : 91.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.60 (0.24), residues: 1237 helix: 1.60 (0.21), residues: 604 sheet: 0.58 (0.39), residues: 166 loop : 0.71 (0.29), residues: 467 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 340 HIS 0.005 0.001 HIS C 275 PHE 0.019 0.001 PHE C 255 TYR 0.012 0.001 TYR A 758 ARG 0.004 0.000 ARG A 779 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2474 Ramachandran restraints generated. 1237 Oldfield, 0 Emsley, 1237 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2474 Ramachandran restraints generated. 1237 Oldfield, 0 Emsley, 1237 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 1093 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 92 time to evaluate : 1.295 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 364 MET cc_start: 0.7815 (mmt) cc_final: 0.7511 (mmt) REVERT: A 507 ASP cc_start: 0.7518 (t70) cc_final: 0.7007 (t0) REVERT: C 14 SER cc_start: 0.8126 (p) cc_final: 0.7912 (p) REVERT: C 123 MET cc_start: 0.7910 (mmm) cc_final: 0.7590 (mmm) REVERT: C 137 GLN cc_start: 0.7888 (OUTLIER) cc_final: 0.7671 (mt0) REVERT: B 93 PHE cc_start: 0.8489 (m-80) cc_final: 0.7999 (m-80) REVERT: B 105 MET cc_start: 0.8347 (OUTLIER) cc_final: 0.7538 (tpp) outliers start: 13 outliers final: 6 residues processed: 98 average time/residue: 0.1764 time to fit residues: 26.8422 Evaluate side-chains 84 residues out of total 1093 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 76 time to evaluate : 1.238 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 VAL Chi-restraints excluded: chain A residue 296 ILE Chi-restraints excluded: chain A residue 718 LYS Chi-restraints excluded: chain C residue 54 VAL Chi-restraints excluded: chain C residue 137 GLN Chi-restraints excluded: chain C residue 355 MET Chi-restraints excluded: chain B residue 105 MET Chi-restraints excluded: chain B residue 119 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 111 optimal weight: 9.9990 chunk 84 optimal weight: 0.0770 chunk 58 optimal weight: 0.3980 chunk 12 optimal weight: 5.9990 chunk 53 optimal weight: 1.9990 chunk 75 optimal weight: 2.9990 chunk 113 optimal weight: 20.0000 chunk 119 optimal weight: 5.9990 chunk 59 optimal weight: 1.9990 chunk 107 optimal weight: 0.9990 chunk 32 optimal weight: 2.9990 overall best weight: 1.0944 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 88 ASN A 726 GLN A 730 ASN C 162 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8330 moved from start: 0.2871 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.034 10365 Z= 0.295 Angle : 0.809 47.427 13998 Z= 0.345 Chirality : 0.042 0.253 1525 Planarity : 0.004 0.052 1792 Dihedral : 11.518 162.604 1396 Min Nonbonded Distance : 2.027 Molprobity Statistics. All-atom Clashscore : 6.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.81 % Favored : 99.19 % Rotamer: Outliers : 1.57 % Allowed : 8.41 % Favored : 90.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.66 (0.24), residues: 1237 helix: 1.69 (0.21), residues: 605 sheet: 0.57 (0.39), residues: 166 loop : 0.69 (0.29), residues: 466 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 781 HIS 0.010 0.001 HIS B 147 PHE 0.017 0.001 PHE C 255 TYR 0.011 0.001 TYR A 259 ARG 0.003 0.000 ARG C 177 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2474 Ramachandran restraints generated. 1237 Oldfield, 0 Emsley, 1237 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2474 Ramachandran restraints generated. 1237 Oldfield, 0 Emsley, 1237 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 1093 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 80 time to evaluate : 1.335 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 507 ASP cc_start: 0.7532 (t70) cc_final: 0.7009 (t0) REVERT: C 123 MET cc_start: 0.7875 (mmm) cc_final: 0.7596 (mmm) REVERT: C 137 GLN cc_start: 0.7934 (OUTLIER) cc_final: 0.7701 (mt0) REVERT: B 93 PHE cc_start: 0.8499 (m-80) cc_final: 0.8011 (m-80) REVERT: B 105 MET cc_start: 0.8424 (OUTLIER) cc_final: 0.7633 (tpp) outliers start: 17 outliers final: 11 residues processed: 89 average time/residue: 0.2042 time to fit residues: 27.5577 Evaluate side-chains 86 residues out of total 1093 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 73 time to evaluate : 1.215 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 VAL Chi-restraints excluded: chain A residue 88 ASN Chi-restraints excluded: chain A residue 296 ILE Chi-restraints excluded: chain A residue 425 SER Chi-restraints excluded: chain A residue 718 LYS Chi-restraints excluded: chain C residue 64 ILE Chi-restraints excluded: chain C residue 137 GLN Chi-restraints excluded: chain C residue 184 ASP Chi-restraints excluded: chain C residue 236 LEU Chi-restraints excluded: chain C residue 286 ASP Chi-restraints excluded: chain C residue 355 MET Chi-restraints excluded: chain B residue 105 MET Chi-restraints excluded: chain B residue 119 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 99 optimal weight: 0.3980 chunk 68 optimal weight: 4.9990 chunk 1 optimal weight: 0.7980 chunk 89 optimal weight: 0.9990 chunk 49 optimal weight: 0.0980 chunk 102 optimal weight: 0.3980 chunk 82 optimal weight: 0.9990 chunk 0 optimal weight: 5.9990 chunk 61 optimal weight: 0.5980 chunk 107 optimal weight: 1.9990 chunk 30 optimal weight: 2.9990 overall best weight: 0.4580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 88 ASN A 216 ASN C 59 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8279 moved from start: 0.3174 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 10365 Z= 0.164 Angle : 0.771 47.352 13998 Z= 0.320 Chirality : 0.040 0.271 1525 Planarity : 0.003 0.048 1792 Dihedral : 11.233 167.443 1396 Min Nonbonded Distance : 2.038 Molprobity Statistics. All-atom Clashscore : 6.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.65 % Favored : 99.35 % Rotamer: Outliers : 1.48 % Allowed : 8.50 % Favored : 90.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.81 (0.24), residues: 1237 helix: 1.80 (0.21), residues: 612 sheet: 0.61 (0.39), residues: 166 loop : 0.79 (0.30), residues: 459 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 79 HIS 0.008 0.001 HIS B 147 PHE 0.015 0.001 PHE C 255 TYR 0.010 0.001 TYR A 758 ARG 0.003 0.000 ARG C 177 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2474 Ramachandran restraints generated. 1237 Oldfield, 0 Emsley, 1237 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2474 Ramachandran restraints generated. 1237 Oldfield, 0 Emsley, 1237 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 1093 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 88 time to evaluate : 1.241 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 132 MET cc_start: 0.7172 (ttm) cc_final: 0.6854 (tpp) REVERT: A 507 ASP cc_start: 0.7498 (t70) cc_final: 0.6933 (t0) REVERT: B 93 PHE cc_start: 0.8422 (m-80) cc_final: 0.7970 (m-80) REVERT: B 105 MET cc_start: 0.8335 (OUTLIER) cc_final: 0.7458 (tpp) outliers start: 16 outliers final: 9 residues processed: 96 average time/residue: 0.2035 time to fit residues: 29.3940 Evaluate side-chains 86 residues out of total 1093 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 76 time to evaluate : 1.165 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 177 MET Chi-restraints excluded: chain A residue 296 ILE Chi-restraints excluded: chain A residue 425 SER Chi-restraints excluded: chain A residue 718 LYS Chi-restraints excluded: chain C residue 260 THR Chi-restraints excluded: chain C residue 286 ASP Chi-restraints excluded: chain C residue 355 MET Chi-restraints excluded: chain B residue 105 MET Chi-restraints excluded: chain B residue 119 LYS Chi-restraints excluded: chain B residue 121 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 40 optimal weight: 1.9990 chunk 107 optimal weight: 1.9990 chunk 23 optimal weight: 0.5980 chunk 70 optimal weight: 1.9990 chunk 29 optimal weight: 1.9990 chunk 119 optimal weight: 1.9990 chunk 99 optimal weight: 0.0570 chunk 55 optimal weight: 1.9990 chunk 9 optimal weight: 0.0050 chunk 39 optimal weight: 0.5980 chunk 62 optimal weight: 1.9990 overall best weight: 0.6514 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8294 moved from start: 0.3306 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 10365 Z= 0.201 Angle : 0.784 47.344 13998 Z= 0.325 Chirality : 0.041 0.277 1525 Planarity : 0.003 0.051 1792 Dihedral : 11.191 170.312 1396 Min Nonbonded Distance : 1.999 Molprobity Statistics. All-atom Clashscore : 6.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.05 % Favored : 98.95 % Rotamer: Outliers : 1.20 % Allowed : 9.61 % Favored : 89.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.83 (0.24), residues: 1237 helix: 1.85 (0.21), residues: 612 sheet: 0.62 (0.39), residues: 166 loop : 0.74 (0.29), residues: 459 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 781 HIS 0.013 0.001 HIS B 147 PHE 0.014 0.001 PHE C 255 TYR 0.010 0.001 TYR A 263 ARG 0.003 0.000 ARG C 177 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2474 Ramachandran restraints generated. 1237 Oldfield, 0 Emsley, 1237 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2474 Ramachandran restraints generated. 1237 Oldfield, 0 Emsley, 1237 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 1093 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 81 time to evaluate : 1.311 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 203 MET cc_start: 0.8293 (mmm) cc_final: 0.7956 (mmm) REVERT: A 364 MET cc_start: 0.7844 (mmt) cc_final: 0.7520 (mmt) REVERT: A 715 MET cc_start: 0.7293 (ptt) cc_final: 0.6985 (ptt) REVERT: B 93 PHE cc_start: 0.8472 (m-80) cc_final: 0.8029 (m-80) REVERT: B 105 MET cc_start: 0.8339 (OUTLIER) cc_final: 0.7487 (tpp) outliers start: 13 outliers final: 9 residues processed: 85 average time/residue: 0.1984 time to fit residues: 25.8407 Evaluate side-chains 84 residues out of total 1093 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 74 time to evaluate : 1.303 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 177 MET Chi-restraints excluded: chain A residue 296 ILE Chi-restraints excluded: chain A residue 718 LYS Chi-restraints excluded: chain A residue 737 LEU Chi-restraints excluded: chain C residue 260 THR Chi-restraints excluded: chain C residue 286 ASP Chi-restraints excluded: chain B residue 73 MET Chi-restraints excluded: chain B residue 105 MET Chi-restraints excluded: chain B residue 119 LYS Chi-restraints excluded: chain B residue 121 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 115 optimal weight: 8.9990 chunk 13 optimal weight: 1.9990 chunk 68 optimal weight: 5.9990 chunk 87 optimal weight: 0.5980 chunk 67 optimal weight: 0.9990 chunk 100 optimal weight: 0.6980 chunk 66 optimal weight: 2.9990 chunk 119 optimal weight: 10.0000 chunk 74 optimal weight: 2.9990 chunk 72 optimal weight: 0.8980 chunk 55 optimal weight: 2.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8332 moved from start: 0.3330 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 10365 Z= 0.280 Angle : 0.805 47.382 13998 Z= 0.337 Chirality : 0.042 0.280 1525 Planarity : 0.004 0.047 1792 Dihedral : 11.294 173.255 1396 Min Nonbonded Distance : 2.013 Molprobity Statistics. All-atom Clashscore : 6.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.37 % Favored : 98.63 % Rotamer: Outliers : 1.02 % Allowed : 9.89 % Favored : 89.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.70 (0.24), residues: 1237 helix: 1.78 (0.21), residues: 613 sheet: 0.57 (0.39), residues: 166 loop : 0.60 (0.29), residues: 458 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 340 HIS 0.010 0.001 HIS B 147 PHE 0.015 0.001 PHE C 255 TYR 0.011 0.001 TYR A 259 ARG 0.003 0.000 ARG C 177 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2474 Ramachandran restraints generated. 1237 Oldfield, 0 Emsley, 1237 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2474 Ramachandran restraints generated. 1237 Oldfield, 0 Emsley, 1237 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 1093 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 78 time to evaluate : 1.306 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 132 MET cc_start: 0.6949 (tpp) cc_final: 0.6647 (tpp) REVERT: A 203 MET cc_start: 0.8322 (mmm) cc_final: 0.8075 (mmm) REVERT: C 325 MET cc_start: 0.7918 (tpt) cc_final: 0.7697 (tpt) REVERT: B 93 PHE cc_start: 0.8437 (m-80) cc_final: 0.8018 (m-80) REVERT: B 105 MET cc_start: 0.8451 (OUTLIER) cc_final: 0.8168 (mmp) outliers start: 11 outliers final: 10 residues processed: 81 average time/residue: 0.1956 time to fit residues: 24.6096 Evaluate side-chains 84 residues out of total 1093 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 73 time to evaluate : 1.407 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 177 MET Chi-restraints excluded: chain A residue 296 ILE Chi-restraints excluded: chain A residue 718 LYS Chi-restraints excluded: chain C residue 184 ASP Chi-restraints excluded: chain C residue 260 THR Chi-restraints excluded: chain C residue 286 ASP Chi-restraints excluded: chain C residue 355 MET Chi-restraints excluded: chain B residue 73 MET Chi-restraints excluded: chain B residue 105 MET Chi-restraints excluded: chain B residue 119 LYS Chi-restraints excluded: chain B residue 121 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 73 optimal weight: 6.9990 chunk 47 optimal weight: 0.8980 chunk 71 optimal weight: 0.6980 chunk 36 optimal weight: 0.9990 chunk 23 optimal weight: 0.4980 chunk 75 optimal weight: 0.8980 chunk 81 optimal weight: 0.9990 chunk 59 optimal weight: 0.5980 chunk 11 optimal weight: 0.9990 chunk 93 optimal weight: 1.9990 chunk 108 optimal weight: 0.7980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8308 moved from start: 0.3496 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 10365 Z= 0.205 Angle : 0.783 47.341 13998 Z= 0.323 Chirality : 0.041 0.282 1525 Planarity : 0.003 0.047 1792 Dihedral : 11.207 175.412 1396 Min Nonbonded Distance : 2.038 Molprobity Statistics. All-atom Clashscore : 6.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.13 % Favored : 98.87 % Rotamer: Outliers : 1.39 % Allowed : 10.07 % Favored : 88.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.69 (0.24), residues: 1237 helix: 1.77 (0.21), residues: 614 sheet: 0.55 (0.39), residues: 166 loop : 0.62 (0.29), residues: 457 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 340 HIS 0.009 0.001 HIS B 147 PHE 0.019 0.001 PHE A 553 TYR 0.009 0.001 TYR C 188 ARG 0.002 0.000 ARG C 177 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2474 Ramachandran restraints generated. 1237 Oldfield, 0 Emsley, 1237 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2474 Ramachandran restraints generated. 1237 Oldfield, 0 Emsley, 1237 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 1093 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 78 time to evaluate : 1.281 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 132 MET cc_start: 0.7107 (tpp) cc_final: 0.6841 (tpp) REVERT: A 203 MET cc_start: 0.8290 (mmm) cc_final: 0.8070 (mmm) REVERT: A 364 MET cc_start: 0.7784 (mmt) cc_final: 0.7484 (mmt) REVERT: C 325 MET cc_start: 0.7917 (tpt) cc_final: 0.7696 (tpt) REVERT: B 93 PHE cc_start: 0.8423 (m-80) cc_final: 0.8022 (m-80) REVERT: B 105 MET cc_start: 0.8433 (OUTLIER) cc_final: 0.8126 (mmp) outliers start: 15 outliers final: 11 residues processed: 84 average time/residue: 0.2015 time to fit residues: 25.9481 Evaluate side-chains 84 residues out of total 1093 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 72 time to evaluate : 1.312 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 ILE Chi-restraints excluded: chain A residue 177 MET Chi-restraints excluded: chain A residue 296 ILE Chi-restraints excluded: chain A residue 384 THR Chi-restraints excluded: chain A residue 718 LYS Chi-restraints excluded: chain C residue 260 THR Chi-restraints excluded: chain C residue 286 ASP Chi-restraints excluded: chain C residue 355 MET Chi-restraints excluded: chain B residue 73 MET Chi-restraints excluded: chain B residue 105 MET Chi-restraints excluded: chain B residue 119 LYS Chi-restraints excluded: chain B residue 121 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 114 optimal weight: 10.0000 chunk 104 optimal weight: 0.9980 chunk 111 optimal weight: 9.9990 chunk 67 optimal weight: 5.9990 chunk 48 optimal weight: 0.0170 chunk 87 optimal weight: 0.5980 chunk 34 optimal weight: 0.6980 chunk 100 optimal weight: 0.0570 chunk 105 optimal weight: 0.8980 chunk 110 optimal weight: 0.0980 chunk 73 optimal weight: 4.9990 overall best weight: 0.2936 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 568 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8261 moved from start: 0.3769 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 10365 Z= 0.141 Angle : 0.778 47.307 13998 Z= 0.316 Chirality : 0.039 0.285 1525 Planarity : 0.003 0.046 1792 Dihedral : 11.075 178.060 1396 Min Nonbonded Distance : 2.099 Molprobity Statistics. All-atom Clashscore : 6.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.97 % Favored : 99.03 % Rotamer: Outliers : 0.83 % Allowed : 10.91 % Favored : 88.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.85 (0.24), residues: 1237 helix: 1.94 (0.22), residues: 605 sheet: 0.56 (0.39), residues: 166 loop : 0.68 (0.29), residues: 466 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 79 HIS 0.008 0.001 HIS B 147 PHE 0.014 0.001 PHE C 255 TYR 0.008 0.001 TYR A 758 ARG 0.002 0.000 ARG A 692 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2474 Ramachandran restraints generated. 1237 Oldfield, 0 Emsley, 1237 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2474 Ramachandran restraints generated. 1237 Oldfield, 0 Emsley, 1237 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 1093 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 82 time to evaluate : 1.355 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 364 MET cc_start: 0.7714 (mmt) cc_final: 0.7412 (mmt) REVERT: C 325 MET cc_start: 0.7931 (tpt) cc_final: 0.7700 (tpt) REVERT: B 93 PHE cc_start: 0.8396 (m-80) cc_final: 0.8025 (m-80) REVERT: B 105 MET cc_start: 0.8352 (OUTLIER) cc_final: 0.8024 (mmp) outliers start: 9 outliers final: 5 residues processed: 83 average time/residue: 0.2302 time to fit residues: 29.9052 Evaluate side-chains 83 residues out of total 1093 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 77 time to evaluate : 1.102 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 718 LYS Chi-restraints excluded: chain C residue 286 ASP Chi-restraints excluded: chain C residue 355 MET Chi-restraints excluded: chain B residue 73 MET Chi-restraints excluded: chain B residue 105 MET Chi-restraints excluded: chain B residue 119 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 117 optimal weight: 0.9990 chunk 71 optimal weight: 0.6980 chunk 55 optimal weight: 2.9990 chunk 81 optimal weight: 0.9990 chunk 123 optimal weight: 9.9990 chunk 113 optimal weight: 4.9990 chunk 98 optimal weight: 0.9990 chunk 10 optimal weight: 0.8980 chunk 75 optimal weight: 0.0670 chunk 60 optimal weight: 0.9990 chunk 78 optimal weight: 4.9990 overall best weight: 0.7322 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 568 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8307 moved from start: 0.3686 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 10365 Z= 0.216 Angle : 0.790 47.260 13998 Z= 0.326 Chirality : 0.041 0.286 1525 Planarity : 0.003 0.048 1792 Dihedral : 11.211 179.065 1396 Min Nonbonded Distance : 2.059 Molprobity Statistics. All-atom Clashscore : 6.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.54 % Favored : 98.46 % Rotamer: Outliers : 0.74 % Allowed : 11.55 % Favored : 87.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.81 (0.24), residues: 1237 helix: 1.93 (0.21), residues: 604 sheet: 0.51 (0.40), residues: 167 loop : 0.64 (0.29), residues: 466 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 340 HIS 0.008 0.001 HIS B 147 PHE 0.014 0.001 PHE C 255 TYR 0.009 0.001 TYR A 259 ARG 0.002 0.000 ARG C 147 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2474 Ramachandran restraints generated. 1237 Oldfield, 0 Emsley, 1237 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2474 Ramachandran restraints generated. 1237 Oldfield, 0 Emsley, 1237 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 1093 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 78 time to evaluate : 1.327 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 364 MET cc_start: 0.7723 (mmt) cc_final: 0.7435 (mmt) REVERT: A 715 MET cc_start: 0.7325 (ptt) cc_final: 0.7034 (ptt) REVERT: C 325 MET cc_start: 0.8004 (tpt) cc_final: 0.7654 (tpt) REVERT: B 93 PHE cc_start: 0.8402 (m-80) cc_final: 0.8003 (m-80) REVERT: B 105 MET cc_start: 0.8442 (OUTLIER) cc_final: 0.8111 (mmp) outliers start: 8 outliers final: 5 residues processed: 81 average time/residue: 0.1928 time to fit residues: 24.2859 Evaluate side-chains 79 residues out of total 1093 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 73 time to evaluate : 1.313 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 260 THR Chi-restraints excluded: chain C residue 286 ASP Chi-restraints excluded: chain C residue 355 MET Chi-restraints excluded: chain B residue 73 MET Chi-restraints excluded: chain B residue 105 MET Chi-restraints excluded: chain B residue 119 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 104 optimal weight: 0.5980 chunk 30 optimal weight: 0.8980 chunk 90 optimal weight: 0.0980 chunk 14 optimal weight: 0.7980 chunk 27 optimal weight: 0.5980 chunk 98 optimal weight: 0.6980 chunk 41 optimal weight: 4.9990 chunk 101 optimal weight: 0.8980 chunk 12 optimal weight: 0.9990 chunk 18 optimal weight: 2.9990 chunk 86 optimal weight: 1.9990 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.100495 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3058 r_free = 0.3058 target = 0.068176 restraints weight = 21184.499| |-----------------------------------------------------------------------------| r_work (start): 0.3039 rms_B_bonded: 3.17 r_work: 0.2876 rms_B_bonded: 3.72 restraints_weight: 0.5000 r_work (final): 0.2876 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8171 moved from start: 0.3798 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 10365 Z= 0.181 Angle : 0.791 47.285 13998 Z= 0.325 Chirality : 0.040 0.285 1525 Planarity : 0.003 0.046 1792 Dihedral : 11.128 175.871 1396 Min Nonbonded Distance : 2.076 Molprobity Statistics. All-atom Clashscore : 6.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.13 % Favored : 98.87 % Rotamer: Outliers : 0.46 % Allowed : 12.01 % Favored : 87.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.75 (0.24), residues: 1237 helix: 1.90 (0.21), residues: 609 sheet: 0.52 (0.39), residues: 167 loop : 0.55 (0.29), residues: 461 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 340 HIS 0.008 0.001 HIS B 147 PHE 0.014 0.001 PHE C 255 TYR 0.008 0.001 TYR A 259 ARG 0.003 0.000 ARG C 177 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2172.61 seconds wall clock time: 40 minutes 1.70 seconds (2401.70 seconds total)